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arXiv · 1904.03910

The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks

Bence Agg·Andrea Csaszar·Mate Szalay-Beko·Daniel V. Veres·Reka Mizsei·Peter Ferdinandy·Peter Csermely·Istvan A. Kovacs
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Abstract

Motivation: Network visualizations of complex biological datasets usually result in 'hairball' images, which do not discriminate network modules. Results: We present the EntOptLayout Cytoscape plug-in based on a recently developed network representation theory. The plug-in provides an efficient visualization of network modules, which represent major protein complexes in protein-protein interaction and signalling networks. Importantly, the tool gives a quality score of the network visualization by calculating the information loss between the input data and the visual representation showing a 3- to 25-fold improvement over conventional methods. Availability and implementation: The plug-in (running on Windows, Linux, or Mac OS) and its tutorial (both in written and video forms) can be downloaded freely under the terms of the MIT license from: http://apps.cytoscape.org/apps/entoptlayout. Supplementary data are available at Bioinformatics online. Contact: csermely.peter@med.semmelweis-univ.hu

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Bence Agg, Andrea Csaszar, Mate Szalay-Beko, Daniel V. Veres, Reka Mizsei, Peter Ferdinandy, Peter Csermely, Istvan A. Kovacs. 2019-11-01. The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks. https://doi.org/10.1093/bioinformatics%2Fbtz257

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